text: The method has mainly been developed for detecting the various phenotypes of metastatic castration-resistant prostate cancer. It requires the usage of patient-derived xenografts for enrichment of ctDNA in blood for further analysis. After WGS, the method utilizes the tool Griffin for inspection of local promoter coverage, nucleosome positioning, fragment size analysis, and composite trancription factor binding sites plus open chromatin sites of ctDNA reads. It also checks the histone modifications and applies dimensionality reduction on the found sites to identify putative promoter, enhancer, and gene repressive heterochromatic marks. To interrogate the chromatine phasing, distance between open chromatin regions, the method uses TritonNP, newly developed software, that uses Fourier transforms and band-pass filters. XGBoost is utilized for classification on cancer subtype with using the features detected in previous steps